Small open reading frames associated with morphogenesis are hidden in plant genomes

被引：144

作者：

Hanada, Kousuke ^{[1
,2
,3
]}

Higuchi-Takeuchi, Mieko ^{[1
]}

Okamoto, Masanori ^{[1
,4
]}

Yoshizumi, Takeshi ^{[1
]}

Shimizu, Minami ^{[1
]}

Nakaminami, Kentaro ^{[1
]}

Nishi, Ranko ^{[1
]}

Ohashi, Chihiro ^{[1
]}

Iida, Kei ^{[2
]}

Tanaka, Maho ^{[1
]}

Horii, Yoko ^{[1
]}

Kawashima, Mika ^{[1
]}

Matsui, Keiko ^{[1
]}

Toyoda, Tetsuro ^{[1
,2
]}

Shinozaki, Kazuo ^{[1
]}

Seki, Motoaki ^{[1
]}

Matsui, Minami ^{[1
]}

机构：

[1] RIKEN, Plant Sci Ctr, Yokohama, Kanagawa 2300045, Japan

[2] RIKEN, Bioinformat & Syst Engn Div, Yokohama, Kanagawa 2300045, Japan

[3] Kyushu Inst Technol, Dept Biosci & Bioinformat, Frontier Res Acad Young Researchers, Iizuka, Fukuoka 8208502, Japan

[4] Univ Calif Riverside, Dept Bot & Plant Sci, Ctr Plant Cell Biol, Riverside, CA 92521 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2013年 / 110卷 / 06期

基金：

日本科学技术振兴机构; 日本学术振兴会;

关键词：

transcriptome; phenome; Agilent custom microarray; transgenic plant; peptide hormone; ARABIDOPSIS-THALIANA; SECRETORY PEPTIDE; GENE-EXPRESSION; RNA-SEQ; POLYPEPTIDE; DIFFERENTIATION; OVEREXPRESSION; PROLIFERATION; TRANSCRIPTS; PREDICTION;

D O I：

10.1073/pnas.1213958110

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

It is likely that many small ORFs (sORFs; 30-100 amino acids) are missed when genomes are annotated. To overcome this limitation, we identified similar to 8,000 sORFs with high coding potential in intergenic regions of the Arabidopsis thaliana genome. However, the question remains as to whether these coding sORFs play functional roles. Using a designed array, we generated an expression atlas for 16 organs and 17 environmental conditions among 7,901 identified coding sORFs. A total of 2,099 coding sORFs were highly expressed under at least one experimental condition, and 571 were significantly conserved in other land plants. A total of 473 coding sORFs were overexpressed; similar to 10% (49/473) induced visible pheno-typic effects, a proportion that is approximately seven times higher than that of randomly chosen known genes. These results indicate that many coding sORFs hidden in plant genomes are associated with morphogenesis. We believe that the expression atlas will contribute to further study of the roles of sORFs in plants.

引用

页码：2395 / 2400

页数：6

共 50 条

[1] Improved scoring of functional groups from gene expression data by decorrelating GO graph structure [J].

Alexa, Adrian ;

Rahnenfuehrer, Joerg ;

Lengauer, Thomas .

BIOINFORMATICS, 2006, 22 (13) :1600-1607

[2] Tyrosine-sulfated glycopeptide involved in cellular proliferation and expansion in Arabidopsis [J].

Amano, Yukari ;

Tsubouchi, Hiroko ;

Shinohara, Hidefumi ;

Ogawa, Mari ;

Matsubayashi, Yoshikatsu .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (46) :18333-18338

[3] INFLORESCENCE DEFICIENT IN ABSCISSION controls floral organ abscission in arabidopsis and identifies a novel family of putative ligands in plants [J].

Butenko, MA ;

Patterson, SE ;

Grini, PE ;

Stenvik, GE ;

Amundsen, SS ;

Mandal, A ;

Aalen, RB .

PLANT CELL, 2003, 15 (10) :2296-2307

[4] Discovery and revision of Arabidopsis genes by proteogenomics [J].

Castellana, Natalie E. ;

Payne, Samuel H. ;

Shen, Zhouxin ;

Stanke, Mario ;

Bafna, Vineet ;

Briggs, Steven P. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (52) :21034-21038

[5] Small Open Reading Frames: Current Prediction Techniques and Future Prospect [J].

Cheng, Haoyu ;

Chan, Wai Soon ;

Li, Zhixiu ;

Wang, Dan ;

Liu, Song ;

Zhou, Yaoqi .

CURRENT PROTEIN & PEPTIDE SCIENCE, 2011, 12 (06) :503-507

[6] Floral dip:: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana [J].

Clough, SJ ;

Bent, AF .

PLANT JOURNAL, 1998, 16 (06) :735-743

[7] SYSTEMIN ACTIVATES SYNTHESIS OF WOUND-INDUCIBLE TOMATO LEAF POLYPHENOL OXIDASE VIA THE OCTADECANOID DEFENSE SIGNALING PATHWAY [J].

CONSTABEL, CP ;

BERGEY, DR ;

RYAN, CA .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1995, 92 (02) :407-411

[8] BRICK1/HSPC300 functions with SCAR and the ARP2/3 complex to regulate epidermal cell shape in Arabidopsis [J].

Djakovic, S ;

Dyachok, J ;

Burke, M ;

Frank, MJ ;

Smith, LG .

DEVELOPMENT, 2006, 133 (06) :1091-1100

[9] An integrated encyclopedia of DNA elements in the human genome [J].

Dunham, Ian ;

Kundaje, Anshul ;

Aldred, Shelley F. ;

Collins, Patrick J. ;

Davis, CarrieA. ;

Doyle, Francis ;

Epstein, Charles B. ;

Frietze, Seth ;

Harrow, Jennifer ;

Kaul, Rajinder ;

Khatun, Jainab ;

Lajoie, Bryan R. ;

Landt, Stephen G. ;

Lee, Bum-Kyu ;

Pauli, Florencia ;

Rosenbloom, Kate R. ;

Sabo, Peter ;

Safi, Alexias ;

Sanyal, Amartya ;

Shoresh, Noam ;

Simon, Jeremy M. ;

Song, Lingyun ;

Trinklein, Nathan D. ;

Altshuler, Robert C. ;

Birney, Ewan ;

Brown, James B. ;

Cheng, Chao ;

Djebali, Sarah ;

Dong, Xianjun ;

Dunham, Ian ;

Ernst, Jason ;

Furey, Terrence S. ;

Gerstein, Mark ;

Giardine, Belinda ;

Greven, Melissa ;

Hardison, Ross C. ;

Harris, Robert S. ;

Herrero, Javier ;

Hoffman, Michael M. ;

Iyer, Sowmya ;

Kellis, Manolis ;

Khatun, Jainab ;

Kheradpour, Pouya ;

Kundaje, Anshul ;

Lassmann, Timo ;

Li, Qunhua ;

Lin, Xinying ;

Marinov, Georgi K. ;

Merkel, Angelika ;

Mortazavi, Ali .

NATURE, 2012, 489 (7414) :57-74

[10] Genome-wide mapping of alternative splicing in Arabidopsis thaliana [J].

Filichkin, Sergei A. ;

Priest, Henry D. ;

Givan, Scott A. ;

Shen, Rongkun ;

Bryant, Douglas W. ;

Fox, Samuel E. ;

Wong, Weng-Keen ;

Mockler, Todd C. .

GENOME RESEARCH, 2010, 20 (01) :45-58

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